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secr (version 4.6.6)

Spatially Explicit Capture-Recapture

Description

Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

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Version

Install

install.packages('secr')

Monthly Downloads

1,470

Version

4.6.6

License

GPL (>= 2)

Issues

Pull Requests

Stars

Forks

Repository

https://github.com/MurrayEfford/secr/

Homepage

https://www.otago.ac.nz/density/

Maintainer

Murray Efford

Last Published

February 29th, 2024

Functions in secr (4.6.6)

Density Surfaces

Coefficient of Variation

Estimate overdispersion

Model Compatibility

Frequently Asked Questions, And Others

Import or export data

Construct Density Design Data

Convert Data To Or From BUGS Format

Plot Likelihood Surface

Compare SECR Models

Convert Data to RMark Input Format

Multi-core Processing

RSE from Fitted Model

Telemetry Fixes in Polygons

Smoothed Resource Surface

Likelihood Ratio Test

Combine Telemetry and Detection Data

Add Covariates to Mask or Traps

Mark-resight Data

Orongorongo Valley Brushtail Possums

Add Binned Covariate

Dissect Spatial Capture History Object

Spatial Capture History Object

Coerce ppp object to popn

Circular Probability

Coerce traps object to mask

Coerce capthist to Data Frame

Initial Parameter Values for SECR

Closed population estimates

Covariates Attribute

Overdispersion of Activity Centres

Array of Parameter Estimates

Coefficients of secr Object

Detector Clustering

Deermouse Live-trapping Datasets

Contour Detection Probability

House mouse live trapping data

Profile Likelihood Confidence Intervals

deleteMaskPoints

Edit Mask Points

Rasterize Area Search or Transect Data

Distance To Nearest Detector

Derived Parameters of Fitted SECR Model

Detection Functions

Confidence Ellipses

Deviance of fitted secr model and residual degrees of freedom

Empirical Variance of H-T Density Estimate

Detail Specification for secr.fit

Home Range Statistics

Simulated Movements

Construct Grid Cells

Expected Number of Individuals

Activity Centres of Detected and Undetected Animals

First or Last Part of an Object

Mask Buffer Diagnostic Plot

Mask Buffer Diagnostic Plot (internal)

Probability Density of Home Range Centre

Hybrid Mixture Model

Logit Transformation

Flat-tailed Horned Lizard Dataset

Construct capthist Object

Multinomial Coefficient of SECR Likelihood

Build Habitat Mask

make.systematic

Construct Systematic Detector Design

Fit Multiple SECR Models

Combine or Split Sessions of capthist Object

Construct Lacework Detector Design

Initial Parameter Values

Build Detector Array

Work with Open Population data

Build Detector Array on Triangular or Hexagonal Grid

Multi-session Objects

Averaging of SECR Models Using Akaike's Information Criterion

Non-target Data

Key to Petal Plot

Outline Around Mask Cells

Plot traps Object

Plot Population Object

Plot Detection Functions

Mask Diagnostics

Ovenbird Mist-netting Dataset

Net Detection Probability

Plot Detection Histories

Mixture Model Check

Ovenbird Acoustic Dataset

Plot Habitat Mask, Density or Resource Surface

Population Object

pointsInPolygon

Points Inside Polygon

Brushtail Possum Trapping Dataset

SECR Model Predictions

Random Landscape

Area of Polygon(s)

Print Detectors

Print or Summarise secr Object

Print Detections

predictDsurface

Predict Density Surface

Combine popn Objects

Read Habitat Mask From File

Combine Columns

Combine capthist Objects

reduce.capthist

Combine Occasions Or Detectors

Combine traps Objects

rectangularMask

Rectangular Mask

Read Detector Data From File

Create a RasterLayer Object from Mask or Dsurface

Import Telemetry Fixes

Defunct Functions in Package secr

Create Default Design Data

Construct Detection Model Design Matrices and Lookups

Internal Functions

Spatially Explicit Capture--Recapture Models

Goodness-of-Fit Test

Score Test for SECR Models

Population Size

Number of Threads

secr-deprecated

Deprecated Functions in Package secr

shareFactorLevels

Fix Inconsistent Covariates

SECR Models Fitted to Demonstration Data

Sighting Attributes

Reformat Signal Data

Simulate Detection Histories

Goodness-of-fit Test Results

Spatially Explicit Capture--Recapture

Random Number Seed

Slice Transect Into Shorter Sections

Detector or Mask Spacing

Simulate 2-D Population

Simulate From Fitted secr Model

Sort Rows of capthist or mask Object

Colour Strip Legend

subset.capthist

Subset or Split capthist Object

Subset, Split or Combine Mask Objects

Subset popn Object

Subset traps Object

Skink Pitfall Data

Mask Buffer Width

Smooth Terms in SECR Models

summary.capthist

Summarise Detections

Time-varying Covariates

Summarise Detector Array

Update Old capthist Format

Specifying a Dynamic Population

transformations

Transform Point Array

Summarise Simulated Population

Summarise Habitat Mask

Troubleshooting

Problems in Fitting SECR Models

Detector Attributes

Complex Detector Layouts

Utility Functions

Plot usage, detections or sightings.

Check SECR Data

Drop Unwanted List Components

Variance - Covariance Matrix of SECR Parameters

Non-Euclidean Distances

Write Data to Text File